Geogenic contamination of groundwater presents a substantial threat to the enduring production and sustainability of irrigated fruit orchards, especially in arid and semi-arid regions where over 60% of horticultural irrigation depends on groundwater sources. Groundwater quality is increasingly threatened by geogenic contamination, presenting a critical global issue. Geogenic contaminants, such as fluoride and arsenic, combined with agricultural practices and inadequate wastewater treatment, pose a significant threat to groundwater. Concentrations of elements including arsenic, fluoride, boron, iron, and sodium often exceed acceptable thresholds. For instance, arsenic (As) levels up to 0.5 ppm have been reported in parts of South Asia, far exceeding the WHO guidelines limit of 0.01 mg/L. Boron concentrations above 2.0 ppm and fluoride concentrations exceeding 1.5 ppm are prevalent in impacted aquifers. Pollution consequences are far reaching, impacting agricultural ecosystems and human health as polluted water infiltrates the food chain via irrigation. These challenges are compounded by climate change and water scarcity, which further strain water sources, including those used in agriculture. Addressing groundwater contamination requires a multi-faceted approach. Strategies include developing crops that can tolerate toxicants, improving irrigation techniques, and employing advanced wastewater treatment technologies. This study solidifies current knowledge concerning the uptake processes and physiological effects of various pollutants in fruit crops. This review emphasizes the synergistic toxicity of many pollutants, identifies gaps in knowledge in species-specific tolerance, and emphasizes the dearth of comprehensive mitigating frameworks. Potential solutions, such as salt-tolerant rootstocks, gypsum amendments, and alternative irrigation timing, are examined to enhance resilient orchard systems in geogenically challenged areas.